The threat to global water resource degradation during the20th century and in the first decade of the21st century has forced environmental and geological scientists to intensify their research into the integration of biological processes with hydrological science(Bonacci et al.,2009).The pattern and intensity of hydrological variability can significantly influence biotic assemblages and their activities(Zalewski et al.,1997),while biotic assemblages may inversely regulate abiotic features(Mitsch and Gosselink,2007).Such processes were studied extensively in surface ecosystems,i.e.rivers and lakes.On some occasions,groundwater microbes were also applied as quality indicators(Hancock et al.,2005;Griebler and Lueders,2009).However in porous or fractured aquifers such studies remain less frequent(Hancock et al.,2005).In this article,the epikarst ecosystem,i.e.perched aquifer,the shallow fissured layer near the karst surface,is discussed.